Regexpcount, a symbolic package for counting problems on regular expressions and words

Issue title: Computing Patterns in Strings

Article type: Research Article

Authors: Nicodème, Pierre

Affiliations: LIX - École polytechnique, 91128 Palaiseau cedex, France

Abstract: In previous work [10], we considered algorithms related to the statistics of matches with words and regular expressions in texts generated by Bernoulli or Markov sources. In this work these algorithms are extended for two purposes: to determine the statistics of simultaneous counting of different motifs, and to compute the waiting time for the first match with a motif in a model which may be constrained. This extension also handles matches with errors. The package is fully implemented and gives access to high and low level commands. We also consider an example corresponding to a practical biological problem: getting the statistics for the number of matches of words of size 8 in a genome (a Markovian sequence), knowing that an (overrepresented DNA protecting) pattern named Chi occurs a given number of times.

Keywords: Marked automata, generating functions, computer algebra

Journal: Fundamenta Informaticae, vol. 56, no. 1-2, pp. 71-88, 2003